The Chemical Structures project aims to provide a
complete set of 3D molecular structures in CML
format. As CML format permits structural data and
many properties to be included, each file also
contains additional information, like molecular
weight, boiling point, melting point, or InChI
code. Data can be explored with a CML-aware
software, like Jmol, or by using a Web browser.

Zeobuilder is a user-friendly GUI toolkit for the
construction of advanced molecular models. It is
extensible via a plugin framework and contains
several advanced tools for building, aligning,
manipulating, and analyzing molecular structures.
It describes a molecular model with a hierarchical
data-structure of reference frames. This
facilitates operations on models at different
levels of detail.

COPASI is a software application for modeling and simulation of biochemical networks. The software package has a GUI that lets users define biochemical network models by entering chemical reactions and kinetic equations. A powerful simulation engine can then perform simulations of the dynamics of the networks and carry out many different computational analyses. COPASI can simulate dynamics using either an ODE approach or a stochastic chemical kinetics approach (Gillespie-type algorithms).

ChemDoodle is a fully functional chemical drawing
application. In addition to being multi-platform,
it natively reads and writes many common file
formats, including ChemDraw's CDX and CDXML. It
provides a number of widgets, a complete
templating system, and access to public databases
of common molecules.

Cain performs stochastic and deterministic
simulations of chemical reactions. It can spawn
multiple simulation processes to utilize
multi-core computers. It stores models, simulation
parameters, and simulation results (populations
and reaction counts) in an XML format. In
addition, SBML models can be imported and
exported. The models and simulation parameters
can be read from input files or edited within the
program. Solvers are implemented as command line
executables, which makes it easy to launch batch
jobs and simplifies the process of adding new
solvers. Solvers include Gillespie's direct
method, Gillespie's first reaction method, Gibson
and Bruck's next reaction method, Tau-leaping, and
Hybrid direct/tau-leaping.

WavePacket is a MatLab program package for
simulating quantum-mechanical wavepacket dynamics,
optionally interacting with electric fields, and
with animated graphics. Being highly versatile, it
can be used mainly in (photoinduced) physics and
chemistry.